Super-dominant pathobiontic bacteria in the nasopharyngeal microbiota as causative agents of secondary bacterial infection in influenza patients
The source of secondary lower respiratory tract bacterial infections in influenza patients is not fully understood. A case–control study was conducted during the 2017–2018 influenza epidemic period in Beijing, China. Nasopharyngeal swabs were collected from 52 virologically confirmed influenza patie...
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| Format: | Article |
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Taylor & Francis Group
2020-01-01
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| Series: | Emerging Microbes and Infections |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/22221751.2020.1737578 |
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| author | Tian Qin Taoran Geng Haijian Zhou Yang Han Hongyu Ren Zhifeng Qiu Xudong Nie Tiekuan Du Junrong Liang Pengcheng Du Wei Jiang Taisheng Li Jianguo Xu |
| author_facet | Tian Qin Taoran Geng Haijian Zhou Yang Han Hongyu Ren Zhifeng Qiu Xudong Nie Tiekuan Du Junrong Liang Pengcheng Du Wei Jiang Taisheng Li Jianguo Xu |
| author_sort | Tian Qin |
| collection | DOAJ |
| description | The source of secondary lower respiratory tract bacterial infections in influenza patients is not fully understood. A case–control study was conducted during the 2017–2018 influenza epidemic period in Beijing, China. Nasopharyngeal swabs were collected from 52 virologically confirmed influenza patients and 24 healthy medical staff. The nasopharyngeal microbiota taxonomic composition was analysed using high-throughput sequencing of the 16S rRNA gene V3–V4 regions. The super-dominant pathobiontic bacterial genus (SDPG) was defined as that accounting for >50% of sequences in a nasopharyngeal swab. We attempted to isolate bacteria of this genus from both nasopharyngeal swabs and lower-respiratory tract samples and analyse their genetic similarities. We observed a significantly lower taxonomy richness in influenza cases compared with healthy controls. A SDPG was detected in 61% of severe cases but in only 24% of mild cases and 29% of healthy controls. In 10 cases, the species isolated from lower-respiratory tract infection sites were identified as belonging to the nasopharyngeal microbiota SDPG. Genetically identical strains were isolated from both nasopharyngeal swabs and lower-respiratory tract infection sites, including 23 Acinetobacter baumannii strains from six severe cases, six Klebsiella pneumoniae strains from two severe cases, five Pseudomonas aeruginosa strains from one severe and one mild case, and four Corynebacterium striatum strains from two severe cases. The SDPG in the nasopharyngeal microbiota are the likely cause of subsequent infection in influenza patients. |
| format | Article |
| id | doaj-art-fa3f0ef87f0d4f518fcddfe005f3e1e4 |
| institution | DOAJ |
| issn | 2222-1751 |
| language | English |
| publishDate | 2020-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Emerging Microbes and Infections |
| spelling | doaj-art-fa3f0ef87f0d4f518fcddfe005f3e1e42025-08-20T03:08:32ZengTaylor & Francis GroupEmerging Microbes and Infections2222-17512020-01-019160561510.1080/22221751.2020.1737578Super-dominant pathobiontic bacteria in the nasopharyngeal microbiota as causative agents of secondary bacterial infection in influenza patientsTian Qin0Taoran Geng1Haijian Zhou2Yang Han3Hongyu Ren4Zhifeng Qiu5Xudong Nie6Tiekuan Du7Junrong Liang8Pengcheng Du9Wei Jiang10Taisheng Li11Jianguo Xu12State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of ChinaDepartment of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of ChinaDepartment of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of ChinaDepartment of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of ChinaDepartment of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of ChinaBeijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of ChinaDepartment of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of ChinaDepartment of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of ChinaThe source of secondary lower respiratory tract bacterial infections in influenza patients is not fully understood. A case–control study was conducted during the 2017–2018 influenza epidemic period in Beijing, China. Nasopharyngeal swabs were collected from 52 virologically confirmed influenza patients and 24 healthy medical staff. The nasopharyngeal microbiota taxonomic composition was analysed using high-throughput sequencing of the 16S rRNA gene V3–V4 regions. The super-dominant pathobiontic bacterial genus (SDPG) was defined as that accounting for >50% of sequences in a nasopharyngeal swab. We attempted to isolate bacteria of this genus from both nasopharyngeal swabs and lower-respiratory tract samples and analyse their genetic similarities. We observed a significantly lower taxonomy richness in influenza cases compared with healthy controls. A SDPG was detected in 61% of severe cases but in only 24% of mild cases and 29% of healthy controls. In 10 cases, the species isolated from lower-respiratory tract infection sites were identified as belonging to the nasopharyngeal microbiota SDPG. Genetically identical strains were isolated from both nasopharyngeal swabs and lower-respiratory tract infection sites, including 23 Acinetobacter baumannii strains from six severe cases, six Klebsiella pneumoniae strains from two severe cases, five Pseudomonas aeruginosa strains from one severe and one mild case, and four Corynebacterium striatum strains from two severe cases. The SDPG in the nasopharyngeal microbiota are the likely cause of subsequent infection in influenza patients.https://www.tandfonline.com/doi/10.1080/22221751.2020.1737578Influenza patientslower-respiratory tract infectionnasopharyngeal microbiota16S rRNA V3–V4super-dominant pathobiontic genus |
| spellingShingle | Tian Qin Taoran Geng Haijian Zhou Yang Han Hongyu Ren Zhifeng Qiu Xudong Nie Tiekuan Du Junrong Liang Pengcheng Du Wei Jiang Taisheng Li Jianguo Xu Super-dominant pathobiontic bacteria in the nasopharyngeal microbiota as causative agents of secondary bacterial infection in influenza patients Emerging Microbes and Infections Influenza patients lower-respiratory tract infection nasopharyngeal microbiota 16S rRNA V3–V4 super-dominant pathobiontic genus |
| title | Super-dominant pathobiontic bacteria in the nasopharyngeal microbiota as causative agents of secondary bacterial infection in influenza patients |
| title_full | Super-dominant pathobiontic bacteria in the nasopharyngeal microbiota as causative agents of secondary bacterial infection in influenza patients |
| title_fullStr | Super-dominant pathobiontic bacteria in the nasopharyngeal microbiota as causative agents of secondary bacterial infection in influenza patients |
| title_full_unstemmed | Super-dominant pathobiontic bacteria in the nasopharyngeal microbiota as causative agents of secondary bacterial infection in influenza patients |
| title_short | Super-dominant pathobiontic bacteria in the nasopharyngeal microbiota as causative agents of secondary bacterial infection in influenza patients |
| title_sort | super dominant pathobiontic bacteria in the nasopharyngeal microbiota as causative agents of secondary bacterial infection in influenza patients |
| topic | Influenza patients lower-respiratory tract infection nasopharyngeal microbiota 16S rRNA V3–V4 super-dominant pathobiontic genus |
| url | https://www.tandfonline.com/doi/10.1080/22221751.2020.1737578 |
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